I had my 3ds connected to my computer via wifi and can access the sd card, but no where can I find the save data. Do the save files have a .sav extension? When I can access the sd card the only files I see are files ending with a .app or .cmp extension. The save file I'm trying to transfer is from SMT IV:apocalypse, retail. The game gives you one save file on the game cartridge and the rest of your save slots are saved on the sd card so I'm thinking the save file should be on the sd card.

 

The saves are on your SD card, but they are compressed; you won't find them easily. Also, most save files are not .sav, that's only used commonly in emulators. As @windhazard said, get JKSM and homebrew launcher. However, saves that are on the SD card are, to my knowledge, saved in the Ext Data, so do an Ext Data backup and not a Save Data backup.
What, might I ask, are you backing up the saves for?

 

It's the easiest if you don't want to use CFW, which takes time to set up.

 

Ok nevermind, I put homebrew on my 3ds and used the JKSM program to back up my save and then transfer it to my pc. One question though, that JKSM program seems to have back up only 1 of my saves from my game. I have two saves, slot 1 is on the game cartridge and slot 2 is on the sd card. Only slot 1 got backed up which isn't a problem, but just curious is it possible to choose which save you want to back up and restore?

 

oh ok, cool. Thank you.